Testing reference genes for transcript profiling in Uromyces appendiculatus during urediospore infection of common bean.
Identifieur interne : 000036 ( Main/Exploration ); précédent : 000035; suivant : 000037Testing reference genes for transcript profiling in Uromyces appendiculatus during urediospore infection of common bean.
Auteurs : Tobias I. Link [Allemagne]Source :
- PloS one [ 1932-6203 ] ; 2020.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Basidiomycota (génétique), Basidiomycota (physiologie), Gènes fongiques (MeSH), Interactions hôte-pathogène (MeSH), Maladies des plantes (microbiologie), Phaseolus (microbiologie), Régulation de l'expression des gènes fongiques (MeSH), Transcriptome (MeSH).
- MESH :
- génétique : Basidiomycota.
- microbiologie : Maladies des plantes, Phaseolus.
- physiologie : Basidiomycota.
- Analyse de profil d'expression de gènes, Gènes fongiques, Interactions hôte-pathogène, Régulation de l'expression des gènes fongiques, Transcriptome.
English descriptors
- KwdEn :
- MESH :
- genetics : Basidiomycota.
- microbiology : Phaseolus, Plant Diseases.
- physiology : Basidiomycota.
- Gene Expression Profiling, Gene Expression Regulation, Fungal, Genes, Fungal, Host-Pathogen Interactions, Transcriptome.
Abstract
Uromyces appendiculatus is a major pathogen on common bean. Like other rust fungi, it uses effectors to influence its host plant. Effectors are assumed to possess characteristic expression profiles, reflecting their activity during the infection process. In order to determine expression profiles using RT-qPCR, stably expressed reference genes are necessary for normalization. These reference genes need to be tested. Using samples representing seven different developmental stages of the urediospore-based infection process we employed RT-qPCR to measure the expression of 14 candidate reference genes and determined the most suitable ones based on the range of Cq values and comparative calculations using the geNorm and NormFinder algorithms. Among the tested genes RPS14 had the smallest Cq range, followed by Elf1a and Elf3; geNorm rated Tub and UbcE2 best with CytB as a third and NormFinder found UbcE2, Tub and Elf3 as best reference genes. Combining these findings using equal weight for the rankings UbcE2, Elf3 and Tub can be considered the best reference genes. A combination of either two reference genes, UbcE2 and Tub or three reference genes, UbcE2, Tub, and Elf3 is recommended for normalization. However, differences between most genes were relatively small, so all tested genes can be considered suitable for normalization with the exception of RPS9, SDH, Ubc and PDK.
DOI: 10.1371/journal.pone.0237273
PubMed: 32760134
PubMed Central: PMC7410203
Affiliations:
Links toward previous steps (curation, corpus...)
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Link</name><affiliation wicri:level="4"><nlm:affiliation>Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Stuttgart</region><settlement type="city">Stuttgart</settlement></placeName><orgName type="university">Université de Hohenheim</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32760134</idno><idno type="pmid">32760134</idno><idno type="doi">10.1371/journal.pone.0237273</idno><idno type="pmc">PMC7410203</idno><idno type="wicri:Area/Main/Corpus">000160</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000160</idno><idno type="wicri:Area/Main/Curation">000160</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000160</idno><idno type="wicri:Area/Main/Exploration">000160</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Testing reference genes for transcript profiling in Uromyces appendiculatus during urediospore infection of common bean.</title><author><name sortKey="Link, Tobias I" sort="Link, Tobias I" uniqKey="Link T" first="Tobias I" last="Link">Tobias I. 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Like other rust fungi, it uses effectors to influence its host plant. Effectors are assumed to possess characteristic expression profiles, reflecting their activity during the infection process. In order to determine expression profiles using RT-qPCR, stably expressed reference genes are necessary for normalization. These reference genes need to be tested. Using samples representing seven different developmental stages of the urediospore-based infection process we employed RT-qPCR to measure the expression of 14 candidate reference genes and determined the most suitable ones based on the range of Cq values and comparative calculations using the geNorm and NormFinder algorithms. Among the tested genes RPS14 had the smallest Cq range, followed by Elf1a and Elf3; geNorm rated Tub and UbcE2 best with CytB as a third and NormFinder found UbcE2, Tub and Elf3 as best reference genes. Combining these findings using equal weight for the rankings UbcE2, Elf3 and Tub can be considered the best reference genes. A combination of either two reference genes, UbcE2 and Tub or three reference genes, UbcE2, Tub, and Elf3 is recommended for normalization. However, differences between most genes were relatively small, so all tested genes can be considered suitable for normalization with the exception of RPS9, SDH, Ubc and PDK.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32760134</PMID><DateCompleted><Year>2020</Year><Month>10</Month><Day>08</Day></DateCompleted><DateRevised><Year>2020</Year><Month>10</Month><Day>08</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>8</Issue><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Testing reference genes for transcript profiling in Uromyces appendiculatus during urediospore infection of common bean.</ArticleTitle><Pagination><MedlinePgn>e0237273</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0237273</ELocationID><Abstract><AbstractText>Uromyces appendiculatus is a major pathogen on common bean. Like other rust fungi, it uses effectors to influence its host plant. Effectors are assumed to possess characteristic expression profiles, reflecting their activity during the infection process. In order to determine expression profiles using RT-qPCR, stably expressed reference genes are necessary for normalization. These reference genes need to be tested. Using samples representing seven different developmental stages of the urediospore-based infection process we employed RT-qPCR to measure the expression of 14 candidate reference genes and determined the most suitable ones based on the range of Cq values and comparative calculations using the geNorm and NormFinder algorithms. Among the tested genes RPS14 had the smallest Cq range, followed by Elf1a and Elf3; geNorm rated Tub and UbcE2 best with CytB as a third and NormFinder found UbcE2, Tub and Elf3 as best reference genes. Combining these findings using equal weight for the rankings UbcE2, Elf3 and Tub can be considered the best reference genes. A combination of either two reference genes, UbcE2 and Tub or three reference genes, UbcE2, Tub, and Elf3 is recommended for normalization. However, differences between most genes were relatively small, so all tested genes can be considered suitable for normalization with the exception of RPS9, SDH, Ubc and PDK.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Link</LastName><ForeName>Tobias I</ForeName><Initials>TI</Initials><Identifier Source="ORCID">0000-0002-1014-2905</Identifier><AffiliationInfo><Affiliation>Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart, Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>08</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS 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